Forum:Proteins in bones
In this forum thread we discuss the proteins that have been found in dinosaurs fossils. Progress we make in this thread should be included in the article: Proteins in bones. Soft tissue Have there been any independent studies outside of Schweitzer's team supporting the hypothesis that the proteins and tissues were endogenous? I know about the mosasaur and lufengosaur proteins, but what about the tyrannosaur collagen? Even today, with her studies, there seem to be a lot of skeptics. Here is an article on Wired about the controversy. According to the article, Asara and Schweitzer actually hid a lot of other protein data that matched up with ostrich hemoglobin, which had been studied before in their lab. Jurassic Park Treasury (talk) 05:25, July 23, 2013 (UTC) Have there been any independent studies outside of Schweitzer's team supporting the hypothesis that the proteins and tissues were endogenous? You answered your own question. I know about the mosasaur and lufengosaur proteins Schweitzer's published a new article in 2012 in which they identified new proteins and further proved that those proteins came from within the bone. Lindgren et al. (2011) also proved they found proteins INSIDE the bones. what about the tyrannosaur collagen? Even today, with her studies, there seem to be a lot of skeptics. :Well, I've scanned the article a little. It is from 2009, which isn't really up to date. As I said, Schweitzer published a new article in 2012 which aimed to show that those proteins were endogenous. I'm pretty sure that it is now a consensus that those proteins are endogenous. If you can find criticism from a real scientific journal or magazines like Scientific American or NewScientist after 2011, I'll bother wasting a thought about it. BastionMonk (talk) 20:21, July 23, 2013 (UTC) I copied some of the protein sequences from the 2012 paper and BLASTed them. Two of the Brachylophosaurus actin sequences matched with fungal actin. not bird or reptile actin. Fungi could contaminate the samples, even if the bones were underground. The tyrannosaur collagen may have had similarity to birds, but it also had similarity to amphibians. I know protein code is conserved, but even that denies the fact that MAMMAL protein should have been more similar. The more I investigate this, Schweitzer's methods become more and more pseudoscientific to me. However, the hadrosaur collagens do seem endogenous, since they only have a 60% or so similarity to modern birds. Then again, it also has a 70% similarity to mammals and a 59% similarity to bacteria, which doesn't make sense. It's probably not much to worry about, but still. I know you said that genes stopped evolving 500 million years ago, but bacteria and animals diverged much eariler than that. So why is a species of Bacillus ''showing up on the BLAST list? At the same time, however, as you said, the collagen came from within the bone. And you said BLAST was a crude method. Are there any better ones out there? Jurassic Park Treasury (talk) 03:22, July 24, 2013 (UTC) I copied some of the protein sequences from the 2012 paper and BLASTed them. The sequences are VERY short, making comparisons doubtfull. This is what they wrote: These data support the presence of non-microbial DNA in these dinosaur cells. Actin, tubulin, and histone H4 are all highly conserved, essentially identical over all animals (Bilateria), and indeed the detected sequences for T. rex and B. canadensis are identical to the consensus sequence. Could you show the results for each sequence. Since they are so short, I can't believe there is that much difference between them. If one peptide is different, you can immediately have an 90% difference. Which is just noise. Then again, it also has a 70% similarity to mammals and a 59% similarity to bacteria, which doesn't make sense. That perfectly makes sense. The proteins are very conserved throughout all life-forms. It would have been weird is it had 70% similarity with bacteria and 50% with animals. I know protein code is conserved, but even that denies the fact that MAMMAL protein should have been more similar. No, it isn't. Schweitzer's methods become more and more pseudoscientific to me. You have no right whatsoever to say that. Their methods are very good. You can argue whether their interpretations are right. BastionMonk (talk) 09:21, July 24, 2013 (UTC) I copied some of the protein sequences from the 2012 paper and BLASTed them. Two of the ''Brachylophosaurus actin sequences matched with fungal actin. not bird or reptile actin. I've done a couple of BLAST myself and listed them below. The sequences are 100% in ALLL life forms. 100% similar to fungi, insects and humans. These regions are conserved throughout evolution. Nothing to worry about. They said this in the article. Can you please stop freaking out like this and take your time to carefully look at results. BastionMonk (talk) 09:54, July 24, 2013 (UTC) Protein sequences Actin Sequence: AGFAGDDAPR *BLAST: 100% identical to all sequences in GenBank, including Cladosporium, Mycosphaerella, Trichophyton, Colletotrichum and again Cladosporium. *Interpretation: Sequence remained 100% identical throughout evolution, since it is identical in fungi, bony fish, bivalves and rodents. If this is a dinosaur protein, this sequence is what we would expect to see. :However, fungi still make up the majority of the list. Jurassic Park Treasury (talk) 04:28, July 25, 2013 (UTC) ::All sequences are 100% identical, so I don't think that matters. BastionMonk (talk) 08:02, July 25, 2013 (UTC) ::You're right. I searched for the same sequence in reptiles and birds and it was still there. It also helps us know what type of actin it is. I think it is alpha actin because all sequences from the reptiles and birds that showed the AGFAGDDAPR sequence were labelled as that. Jurassic Park Treasury (talk) 09:36, July 25, 2013 (UTC) Sequence: AVFPSIVGR *BLAST: matches 100% with creatures ranging from Humans to . *Interpretation: This sequence is conserved in all life forms. If this is a dinosaur protein, this is what we would expect to see. alpha-1A Sequence: QXXXXXXXXXXXXXXXXLFHPEQLITGK *BLAST: matches 100% with creatures ranging from Humans to . *Interpretation: This sequence is conserved in all life forms. If this is a dinosaur protein, this is what we would expect to see. Sequence: EIIDLVLDR *BLAST: matches 100% with creatures ranging from Humans to . *Interpretation: This sequence is conserved in all life forms. If this is a dinosaur protein, this is what we would expect to see. Histone H4 Sequence: DAVTYTEHAK *BLAST: 100% identical to all sequences stored in GenBank (couldn't find vertebrates though) *Interpretation: This sequence is probably conserved in all life forms. If this is a dinosaur protein, this is what we would expect to see. Amino Acid sequence:P0C2W2.2, ncbi database 1 gatgapgiag apgfpgarga pgpqgpsgap gpkxxxxxxx xxxxxxxxxx xxxxxxxxxx 61 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 121 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 181 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 241 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxgv qgppgpqgpr 301 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 361 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 421 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxgs agppgatgfp 481 gaagrxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 541 xxxxxxxxxx xxxxxxxxxx xgvvglpgqr * BLAST: Has a 94% similarity to chickens, sea turtles and amphibians, with a 91% similarity to anoles and mammals. * Interpretation: Looking at the BLAST list more closely, this sequence does seem to be endogenous. If this is a dinosaur protein, then the similarity to modern archosaurs is what we'd expect to see. Collagen, type I, alpha 2 Amino Acid sequenceP0C2W4.1, ncbi database: glpgesgavg pagpigsr *BLAST: 100% identity with modern birds, including ducks, pigeons, finches, chickens and collared flycatchers. 94% identity with mammals, and an 88% identity to lizards. *Interpretation: This protein seems to be highly conserved in birds. Since T. rex and birds are both coelurosaurs, I'll give it the benefit of the doubt, but it's a bit hard to tell without sequences from other groups of modern archosaurs first. Amino Acid sequenceP86290.1, ncbi database: gsngepgsag ppgpaglrgl pgesgavgpa gppgsr *BLAST: 67% identity with chickens, ducks, pigeons and turkeys, and a 76% identity with anoles. *Interpretation: This protein seems to be similar throughout all amniotes (reptiles, mammals and birds). If it is a dinosaur protein, the similarity with birds and lizards is what we would expect to see. Amino Acid sequenceP0C2W3.1, ncbi database: 1 glvgapglrg lpgk *BLAST: 100% identity with'' Xenopus'', AKA the African clawed frog. *Interpretation: Oh dear, this one seems more disappointing. Although Schweitzer and Horner said that there were no amphibians in the Hell Creek area, African clawed frogs are common model organisms in labs. Amino Acid sequenceP86289.1, ncbi database: 1 gatgapgiag apgfpgargp sgpqgpsgap gpkgvqgppg pqgprgltgp igppgpagap 61 gdkgeagpsg ppgptgargs agppgatgfp gaagrgetgp agpagppgpa gar *BLAST: 60% identity with chickens, 56% with sea turtles, 58% with anoles, 63% identity with armadillos. *Interpretation: This protein sequence doesn't seem to be as conserved as the others. Due to the better sterilization techniques used for Brachylophosaurus, and the fact that no modern sequence has an exact match to it, I'd say that this is a dinosaur protein. I blasted the rex collagen again, now it also has a 94% similarity to peregrine falcon and painted turtle proteins. This helps confirm the hypothesis that it is endogenous. Jurassic Park Treasury (talk) 06:59, September 9, 2013 (UTC) I BLASTed the T. rex COL1A1, looking for similarities in amphibians only. It had a 100% similarity with Xenopus. Not only is this completely identical, it is higher than the similarity to birds and reptiles. The debate is over. The proteins are contamination. Needless to say, I'm disappointed. Jurassic Park Treasury (talk) 02:09, December 5, 2013 (UTC) EDIT: It seems that BLAST search only covers one part of the sequence. Other parts weren't 100% identical. Bastion, I know you told me to stop freaking out, but I just have a skeptical mind. I know you said the proteins were found inside the bones, but that doesn't rule out contamination if another animal's proteins got inside the bone through reusing used tools. Jurassic Park Treasury (talk) 02:22, December 5, 2013 (UTC) After more comparisons, the contamination hypothesis is raising its ugly head further. The AP part of the amino acid code is found in the frog protein, but not in any bird or reptile collagen. It isn't even found in the Brachylophosaurus collagen (which does appear to be endogenous), which further puts the nail on the coffin. Jurassic Park Treasury (talk) 02:36, December 6, 2013 (UTC) I just BLASTed the region that matched 100% with Xenopus, and only that region. It also matched 100% with birds and alligators. Guess I was just being hysterical. When I BLASTed the whole sequence though, it still gave a 100% match to Xenopus, even though it still only compared those 18 amino acids. When I compared the rex and frog sequences on Notepad, the sequence differed by three amino acids, and the other parts differ even more. I am very confused right now. Could it be a glitch in BLAST, or is it normal? Jurassic Park Treasury (talk) 06:54, December 6, 2013 (UTC) Critic response The Fossil Forum critic said this about deducing a DNA sequence from an amino acid sequence: "No, no, and more no. You can not deduce a DNA sequence from an amino acid sequence. All third base pair variation would be irretrievably lost. Regardless, to what end would this be useful? Sequence data from DNA is useful for several primary reasons. One, it allows us to study the proteins the DNA codes for. Two, we can examine untranslated control regions that dictate how and when proteins are made. Three, genetic studies can compare minor/major DNA differences present between different populations or taxon groups. Assuming you already possessed the amino acid sequence data you would not need the DNA sequence to understand the protein, no untranslated regions would be preserved in the protein, and you can conduct population genetics analysis on amino acid sequences as well as DNA sequences. So again, to what end?" 04:28, March 7, 2014 (UTC) :I can see anything in here something that could disturb you. But, ok, I'll give a response. Thank him for stating the obvious. On this wiki, we are interested in what could help us to clone dinosaurs. Or at least something that closely resembles dinosaurs. I don't give a coprolite (!) what some unknown random guy on the www thinks about that. Protein-derived DNA sequences could help to some extent. * Identify the species of the sample: If we ever found dinosaur DNA. Protein-derived DNA sequences could help to identify its species. * If we would ever create a Chickenosaurus that has the phenotype of a T. rex, it would still have the genes of a chicken. We could give the creature more authenticity by changing its chicken-genes to dinosaur-genes. People already moan because JP's dinosaurs have some frog genes. If you translate AA code back in DNA code, you won't know every 3th nucleotide (except for Tryptophan and Methionine). However, that 3th nucleotide has no biological function. So, if we would insert the wrong nucleotide in our Chickenosaur, it wouldn't matter. BastionMonk (talk) 13:58, March 7, 2014 (UTC) Sources